ijms-logo

Journal Browser

Journal Browser

Special Issue "Horticultural Crop Improvement: A New Era for Plant Molecular Research 2.0"

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 30 January 2024 | Viewed by 2506

Special Issue Editors

College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
Interests: evolution of plant metabolic network; metabolic network reconstruction; biosynthesis of specialized metabolites; regulation of plant metabolism; plant-herbivore interaction; solanaceae; glandular trichome
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Horticultural plants are intensively cultivated crops with high economic value, such as tree fruits, vegetables, ornamental plants, and tea crops. The wide taxonomic distribution and sophisticated domestication history of horticultural crops have led to their highly diverse and complex genomes, which has caused challenges regarding the systematic studies of these plants.

Molecular biology reveals the molecular basis of biological processes in cells, and it is essential for understanding the mechanisms of the execution and regulation of biological processes. Molecular biology technologies have been applied to a wide range of living organisms. However, knowledge about horticultural crops is relatively less available than that on model plants. Recent advances in molecular biology—represented by revolutionary biotechnologies such as plant genome editing and next-generation sequencing—provide unprecedented opportunities to gain insight into the less well-studied horticultural crops.

For this Special Issue, we welcome any original research articles, reviews, short notes, or opinion articles that highlight horticultural crop improvement applications in molecular biology, such as whole-genome resequencing, transcriptomics, proteomics, metabolomics, and genome editing. The topics include, but are not limited to, studies of regulatory mechanisms of plant growth and development, as well as efforts to improve crop yield, quality, and resistance to biotic/abiotic stresses.

Prof. Dr. Bo Sun
Dr. Pengxiang Fan
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • horticultural plants
  • whole-genome resequencing
  • transcriptomics
  • proteomics
  • metabolomics
  • gene editing
  • gene regulation
  • growth and development
  • yield
  • quality
  • resistance

Published Papers (5 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

Article
Comparative Analysis of the Complete Mitochondrial Genomes of Apium graveolens and Apium leptophyllum Provide Insights into Evolution and Phylogeny Relationships
Int. J. Mol. Sci. 2023, 24(19), 14615; https://doi.org/10.3390/ijms241914615 - 27 Sep 2023
Viewed by 150
Abstract
The genus Apium, belonging to the family Apiaceae, comprises roughly 20 species. Only two species, Apium graveolens and Apium leptophyllum, are available in China and are both rich in nutrients and have favorable medicinal properties. However, the lack of genomic data has severely [...] Read more.
The genus Apium, belonging to the family Apiaceae, comprises roughly 20 species. Only two species, Apium graveolens and Apium leptophyllum, are available in China and are both rich in nutrients and have favorable medicinal properties. However, the lack of genomic data has severely constrained the study of genetics and evolution in Apium plants. In this study, Illumina NovaSeq 6000 and Nanopore sequencing platforms were employed to identify the mitochondrial genomes of A. graveolens and A. leptophyllum. The complete lengths of the mitochondrial genomes of A. graveolens and A. leptophyllum were 263,017 bp and 260,164 bp, respectively, and contained 39 and 36 protein-coding genes, five and six rRNA genes, and 19 and 20 tRNA genes. Consistent with most angiosperms, both A. graveolens and A. leptophyllum showed a preference for codons encoding leucine (Leu). In the mitochondrial genome of A. graveolens, 335 SSRs were detected, which is higher than the 196 SSRs found in the mitochondrial genome of A. leptophyllum. Studies have shown that the most common RNA editing type is C-to-U, but, in our study, both A. graveolens and A. leptophyllum exhibited the U-C editing type. Furthermore, the transfer of the mitochondrial genomes of A. graveolens and A. leptophyllum into the chloroplast genomes revealed homologous sequences, accounting for 8.14% and 4.89% of the mitochondrial genome, respectively. Lastly, in comparing the mitochondrial genomes of 29 species, it was found that A. graveolens, A. leptophyllum, and Daucus carota form a sister group with a support rate of 100%. Overall, this investigation furnishes extensive insights into the mitochondrial genomes of A. graveolens and A. leptophyllum, thereby enhancing comprehension of the traits and evolutionary patterns within the Apium genus. Additionally, it offers supplementary data for evolutionary and comparative genomic analyses of other species within the Apiaceae family. Full article
Show Figures

Figure 1

Article
Comparative Transcriptome Analysis of Purple and Green Flowering Chinese Cabbage and Functional Analyses of BrMYB114 Gene
Int. J. Mol. Sci. 2023, 24(18), 13951; https://doi.org/10.3390/ijms241813951 - 11 Sep 2023
Viewed by 273
Abstract
Flowering Chinese cabbage (Brassica rapa var. parachinensis) is one of the most popular vegetables in the south of China. As an antioxidant, anthocyanin is an important quality trait in vegetables, and the gene related to anthocyanin biosynthesis in purple flowering Chinese [...] Read more.
Flowering Chinese cabbage (Brassica rapa var. parachinensis) is one of the most popular vegetables in the south of China. As an antioxidant, anthocyanin is an important quality trait in vegetables, and the gene related to anthocyanin biosynthesis in purple flowering Chinese cabbage is also important. In this study, two flowering Chinese cabbage with extreme colors in the stem were used as materials for transcriptome analysis. RNA-seq analysis showed that 6811 differentially expressed genes (DEGs) were identified, including 295 transcription factors. Phenylpropanoid biosynthesis, flavone and flavanol biosynthesis, and flavonoid biosynthesis pathways were found to be significantly enriched in the purple flowering Chinese cabbage. A total of 25 DEGs associated with anthocyanin biosynthesis were found at a higher expression in purple flowering Chinese cabbage than in green flowering Chinese cabbage. Bioinformatics analysis shows that BrMYB114 is a candidate gene for the regulation of anthocyanin biosynthesis, and heterologous expression analysis of BrMYB114 in Nicotiana benthamiana indicates that BrMYB114 functions in anthocyanin biosynthesis. Therefore, our findings provide vital evidence for elucidating the molecular mechanism in the purple stem in flowering Chinese cabbage. Full article
Show Figures

Figure 1

Article
Effects of sgRNAs, Promoters, and Explants on the Gene Editing Efficiency of the CRISPR/Cas9 System in Chinese Kale
Int. J. Mol. Sci. 2023, 24(17), 13241; https://doi.org/10.3390/ijms241713241 - 26 Aug 2023
Viewed by 454
Abstract
The CRISPR/Cas9 system is extensively used for plant gene editing. This study developed an efficient CRISPR/Cas9 system for Chinese kale using multiple sgRNAs and two promoters to create various CRISPR/Cas9 vectors. These vectors targeted BoaZDS and BoaCRTISO in Chinese kale protoplasts and cotyledons. [...] Read more.
The CRISPR/Cas9 system is extensively used for plant gene editing. This study developed an efficient CRISPR/Cas9 system for Chinese kale using multiple sgRNAs and two promoters to create various CRISPR/Cas9 vectors. These vectors targeted BoaZDS and BoaCRTISO in Chinese kale protoplasts and cotyledons. Transient transformation of Chinese kale protoplasts was assessed for editing efficiency at three BoaZDS sites. Notably, sgRNA: Z2 achieved the highest efficiency (90%). Efficiency reached 100% when two sgRNAs targeted BoaZDS with a deletion of a large fragment (576 bp) between them. However, simultaneous targeting of BoaZDS and BoaCRTISO yielded lower efficiency. Transformation of cotyledons led to Chinese kale mutants with albino phenotypes for boazds mutants and orange-mottled phenotypes for boacrtiso mutants. The mutation efficiency of 35S-CRISPR/Cas9 (92.59%) exceeded YAO-CRISPR/Cas9 (70.97%) in protoplasts, and YAO-CRISPR/Cas9 (96.49%) surpassed 35S-CRISPR/Cas9 (58%) in cotyledons. These findings introduce a strategy for enhancing CRISPR/Cas9 editing efficiency in Chinese kale. Full article
Show Figures

Figure 1

Article
Genome-Wide Analysis of the MADS-box Gene Family and Expression Analysis during Anther Development in Salvia miltiorrhiza
Int. J. Mol. Sci. 2023, 24(13), 10937; https://doi.org/10.3390/ijms241310937 - 30 Jun 2023
Viewed by 593
Abstract
MADS-box genes constitute a large family of transcription factors that play important roles in plant growth and development. However, our understanding of MADS-box genes involved in anther development and male sterility in Salvia miltiorrhiza is still limited. In this study, 63 MADS-box genes [...] Read more.
MADS-box genes constitute a large family of transcription factors that play important roles in plant growth and development. However, our understanding of MADS-box genes involved in anther development and male sterility in Salvia miltiorrhiza is still limited. In this study, 63 MADS-box genes were identified from the genome of the male sterility ecotype Sichuan S. miltiorrhiza (S. miltiorrhiza_SC) unevenly distributed among eight chromosomes. Phylogenetic analysis classified them into two types and 17 subfamilies. They contained 1 to 12 exons and 10 conserved motifs. Evolution analysis showed that segmental duplication was the main force for the expansion of the SmMADS gene family, and duplication gene pairs were under purifying selection. Cis-acting elements analysis demonstrated that the promoter of SmMADS genes contain numerous elements associated with plant growth and development, plant hormones, and stress response. RNA-seq showed that the expression levels of B-class and C-class SmMADS genes were highly expressed during anther development, with SmMADS11 likely playing an important role in regulating anther development and male fertility in S. miltiorrhiza_SC. Overall, this study provides a comprehensive analysis of the MADS-box gene family in S. miltiorrhiza, shedding light on their potential role in anther development and male sterility. Full article
Show Figures

Figure 1

Article
Sequencing and Analysis of Complete Chloroplast Genomes Provide Insight into the Evolution and Phylogeny of Chinese Kale (Brassica oleracea var. alboglabra)
Int. J. Mol. Sci. 2023, 24(12), 10287; https://doi.org/10.3390/ijms241210287 - 17 Jun 2023
Viewed by 745
Abstract
Chinese kale is a widely cultivated plant in the genus Brassica in the family Brassicaceae. The origin of Brassica has been studied extensively, but the origin of Chinese kale remains unclear. In contrast to Brassica oleracea, which originated in the Mediterranean region, [...] Read more.
Chinese kale is a widely cultivated plant in the genus Brassica in the family Brassicaceae. The origin of Brassica has been studied extensively, but the origin of Chinese kale remains unclear. In contrast to Brassica oleracea, which originated in the Mediterranean region, Chinese kale originated in southern China. The chloroplast genome is often used for phylogenetic analysis because of its high conservatism. Fifteen pairs of universal primers were used to amplify the chloroplast genomes of white-flower Chinese kale (Brassica oleracea var. alboglabra cv. Sijicutiao (SJCT)) and yellow-flower Chinese kale (Brassica oleracea var. alboglabra cv. Fuzhouhuanghua (FZHH)) via PCR. The lengths of the chloroplast genomes were 153,365 bp (SJCT) and 153,420 bp (FZHH) and both contained 87 protein-coding genes and eight rRNA genes. There were 36 tRNA genes in SJCT and 35 tRNA genes in FZHH. The chloroplast genomes of both Chinese kale varieties, along with eight other Brassicaceae, were analyzed. Simple sequence repeats, long repeats, and variable regions of DNA barcodes were identified. An analysis of inverted repeat boundaries, relative synonymous codon usage, and synteny revealed high similarity among the ten species, albeit the slight differences that were observed. The Ka/Ks ratios and phylogenetic analysis suggest that Chinese kale is a variant of B. oleracea. The phylogenetic tree shows that both Chinese kale varieties and B. oleracea var. oleracea were clustered in a single group. The results of this study suggest that white and yellow flower Chinese kale comprise a monophyletic group and that their differences in flower color arose late in the process of artificial cultivation. Our results also provide data that will aid future research on genetics, evolution, and germplasm resources of Brassicaceae. Full article
Show Figures

Figure 1

Back to TopTop